Examples:

Many crusades have been fought over the Transformers comics. It doesn't help that the UK comics published stories taking place in between the US issues (which came out much more slowly) without knowing what specifically would happen next. At one point there were three Megatrons running around.

The Whoniverse is such a complete Continuity Snarl that it's only through severe Canon Wank (often in essay form) that people can begin to put things in order.

Star Trek. Sort of. Most of ST's canon is straightforward enough other than that Abrams thing, time paradoxes excepted, which always work out in-arc. The Enterprise relaunch novels may attract this though due to avoiding Trip's death in the last TV episode.

A notable exception is the Trek comic books of the early 80s. i.e. the ones written after Khan without any knowledge of the plot of Search For Spock, where Kirk spends an extended time with Saavik as his science officer because Spock is dead. Even worse are those written after Search with no knowledge of the plot of Voyage Home, where Kirk is captain of the Excelsior, and Spock is captain of another ship, the Surak. Severe wanking ensues.

Any attempt to work out how Sonic the Hedgehog's powers work in relation to physics — albeit a distorted set of physics, due to the conceit of a universe with seven Green Rocks which become an Infinity+1 Sword when their powers are combined. This is not helped by the actual different origin that Sega of America was allowed to come up with (whereas Sonic's speed was an in-born trait according to Sega of Japan, Sonic was the result of a lab experiment by Robotnik's Good Twin via Sega Of America).

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